Recombinase polymerase amplification (RPA) is a highly sensitive and selective isothermal amplification technique, operating at 37–42°C, with minimal sample preparation and capable of amplifying as ...low as 1–10 DNA target copies in less than 20 min. It has been used to amplify diverse targets, including RNA, miRNA, ssDNA and dsDNA from a wide variety of organisms and samples. An ever increasing number of publications detailing the use of RPA are appearing and amplification has been carried out in solution phase, solid phase as well as in a bridge amplification format. Furthermore, RPA has been successfully integrated with different detection strategies, from end-point lateral flow strips to real-time fluorescent detection amongst others. This review focuses on the different methodologies and advances related to RPA technology, as well as highlighting some of the advantages and drawbacks of the technique.
•RPA principles, advantages and limitations.•Comparison of diverse RPA methods: target, label, amplification and detection strategies.•Expected future trends.
Bipolar disorder (BD) is a mood disorder with subtypes characterized by episodes of mania, hypomania, and/or depression. BD is associated with substantial economic burden, and the bipolar I disorder ...(BD-I) subtype is associated with high medical costs. This review further evaluated the economic burden of BD and BD-I in the United States (US), describing health-care resource utilization (HCRU) and sources of direct medical and indirect costs. Data were obtained from systematic searches of MEDLINER, EMBASER, and National Health Service Economic Evaluation Database. Citations were screened to identify primary research studies (published 2008-2018) on the economic burden of BD/BD-I or its treatment in real-world settings. Reported costs were converted to 2018 US dollars. Of identified abstracts (N=4111), 56 studies were included. The estimated total annual national economic burden of BD/BD-I was more than $195 billion, with approximately 25% attributed to direct medical costs. Individuals with BD/BD-I used health-care services more frequently and had higher direct medical costs than matched individuals without the disease. Drivers of higher direct costs included frequent psychiatric interventions, presence of comorbid medical/psychiatric conditions, and both suboptimal medication adherence and clinical management. Indirect costs (eg, unemployment, lost work productivity for patients/caregivers) accounted for 72-80% of the national economic burden of BD/BD-I. Different definitions for study populations and cost categories limited comparisons of economic outcomes. This review builds on existing literature describing the economic burden of BD and confirmed cost drivers of BD/BD-I. Improved clinical management of BD/BD-I and associated comorbidities, together with better medication adherence, may reduce health-care costs and improve patient outcomes. Keywords: cost of illness, health care costs, indirect costs, mania, mood disorder, resource utilization
The importance of histamine in various physiological functions and its involvement in allergenic responses make this small molecule one of the most studied biogenic amines. Even though a variety of ...chromatography-based methods have been described for its analytical determination, the disadvantages they present in terms of cost, analysis time, and low portability limit their suitability for in situ routine testing. In this work, we sought to identify histamine-binding aptamers that could then be exploited for the development of rapid, facile, and sensitive assays for histamine detection suitable for point-of-need analysis. A classic SELEX process was designed employing magnetic beads for target immobilization and the selection was completed after ten rounds. Following Next Generation Sequencing of the last selection rounds from both positive and counter selection magnetic beads, several sequences were identified and initially screened using an apta-PCR affinity assay (APAA). Structural and functional characterization of the candidates resulted in the identification of the H2 aptamer. The high binding affinity of the H2 aptamer to histamine was validated using four independent assays (K D of 3–34 nM). Finally, the H2 aptamer was used for the development of a magnetic beads-based competitive assay for the detection of histamine in both buffer and synthetic urine, achieving very low limits of detection of 18 pM and 76 pM, respectively, while no matrix effects were observed. These results highlight the suitability of the strategy followed for identifying small molecule-binding aptamers and the compatibility of the selected H2 aptamer with the analysis of biological samples, thus facilitating the development of point-of-care devices for routine testing. Ongoing work is focused on extending the application of the H2 aptamer to the detection of spoilage in meat, fish, and beverages, as well as evaluating the affinity of truncated forms of the aptamer.
Isothermal recombinase polymerase amplification-based solid-phase primer extension is used for the optical detection of a hypertrophic cardiomyopathy associated single nucleotide polymorphism (SNP) ...in a fingerprick blood sample. The assay exploits four thiolated primers which have the same sequences with the exception of the 3′-terminal base. Target DNA containing the SNP site hybridizes to all four of the immobilized probes, with primer extension only taking place from the primer containing the terminal base that is complementary to the SNP under interrogation. Biotinylated deoxynucleotide triphosphates are used in the primer extension, allowing postextension addition of streptavidin-poly-horseradish peroxidase to bind to the incorporated biotinylated dNTPs. The signal generated following substrate addition can then be measured optically. The percentage of biotinylated dNTPs and the duration of primer extension is optimized and the system applied to the identification of a SNP in a fingerprick blood sample. A methodology of thermal lysis using a 1 in 5 dilution of the fingerprick blood sample prior to application of 95 °C for 30 s is used to extract genomic DNA, which is directly used as a template for solid-phase primer extension on microtiter plates, followed by optical detection. The SNP in the fingerprick sample was identified and its identity corroborated using ion torrent next generation sequencing. Ongoing work is focused on extension to the multiplexed detection of SNPs in fingerprick and other biological samples.
The objective of this study was to validate the effect of genetic improvement using the Irish genetic merit index, the Economic Breeding Index (EBI), on total lactation performance and lactation ...profiles for milk yield, milk solids yield (fat plus protein; kg), and milk fat, protein, and lactose content within 3 pasture-based feeding treatments (FT) and to investigate whether an interaction exists between genetic group (GG) of Holstein-Friesian and pasture-based FT. The 2 GG were (1) extremely high EBI representative of the top 5% nationally (referred to as the elite group) and (2) representative of the national average EBI (referred to as the NA group). Cows from each GG were randomly allocated each year to 1 of 3 pasture-based FT: control, lower grass allowance, and high concentrate. The effects of GG, FT, year, parity, and the interaction between GG and FT adjusted for calving day of year on milk and milk solids (fat plus protein; kg) production across lactation were studied using mixed models. Cow was nested within GG to account for repeated cow records across years. The overall and stage of lactation-specific responses to concentrate supplementation (high concentrate vs. control) and reduced pasture allowance (lower grass allowance vs. control) were tested. Profiles of daily milk yield, milk solids yield, and milk fat, protein, and lactose content for each week of lactation for the elite and NA groups within each FT and for each parity group within the elite and NA groups were generated. Phenotypic performance was regressed against individual cow genetic potential based on predicted transmitting ability. The NA cows produced the highest milk yield. Milk fat and protein content was higher for the elite group and consequently yield of solids-corrected milk was similar, whereas yield of milk solids tended to be higher for the elite group compared with the NA group. Milk lactose content did not differ between GG. Responses to concentrate supplementation or reduced pasture allowance did not differ between GG. Milk production profiles illustrated that elite cows maintained higher production but with lower persistency than NA cows. Regression of phenotypic performance against predicted transmitting ability illustrated that performance was broadly in line with expectation. The results illustrate that the superiority of high-EBI cattle is consistent across diverse pasture-based FT. The results also highlight the success of the EBI to deliver production performance in line with the national breeding objective: lower milk volume with higher fat and protein content.
Two different DNA (ERBB2c and CD24c) modified gold nanoparticles and graphene oxide loaded on glassy carbon electrodes were prepared for early detection of breast cancer markers by electrochemical ...detection of HER2. Comparative study of ERBB2c and CD24c for the detection was carried out. A “sandwich-type” detection strategy was employed in this electrochemical DNA biosensor and its response was measured by amperometric detection. The electrochemical signal enhancement achieved via gold nanoparticles and grapheme oxide system allowed for sensitive detection of the breast cancer biomarker ERBB2 and the control marker CD24. The modified graphene oxide was characterised using Raman spectroscopy, UV–visible spectroscopy, Fourier transform infrared spectroscopy transmission electron microscopy, scanning electron microscopy and energy-dispersive X-ray spectroscopy. The various steps involved in the modification of a glassy carbon electrode with graphene oxide, gold nanoparticles and DNA probes, target and reporter probe were electrochemically characterised using cyclic voltammetry and electrochemical impedance spectroscopy. Using amperometric detection of a horse radish peroxidase label, detection limits of 0.16nM and 0.23nM were obtained with sensitivity 378nA/nM and 219nA/nM for ERBB2 andCD24 respectively.
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•Gold nanoparticles were linked to graphene oxide and then grafted on to glassy carbon.•Thiolated nucleic acid capture probes were surface immobilized.•The signal enhancement achieved allowed sensitive detection of breast cancer marker ERBB2.•The control marker CD24 was also detected at low concentration.
Using in vitro selection, high affinity DNA aptamers to the food allergen Lup an 1, ß-conglutin, were selected from a pool of DNA, 93 bases in length, containing a randomised sequence of 49 bases. ...ß-conglutin was purified from lupin flour and chemically crosslinked to carboxylated magnetic beads. Peptide mass fingerprinting was used to confirm the presence of the ß-conglutin. Single stranded DNA was generated from the randomised pool using T7 Gene 6 Exonuclease and was subsequently incubated with the magnetic beads and the captured DNA was released and amplified prior to a further round of Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Evolution was monitored using enzyme linked oligonucleotide assay and surface plasmon resonance. Once a plateau in evolution was reached, the isolated DNA sequences were cloned and sequenced. The consensus motif was identified via alignment of the sequences and the affinities of these sequences for immobilised ß-conglutin were determined using surface plasmon resonance. The selected aptamer was demonstrated to be highly specific, showing no cross-reactivity with other flour ingredients or with other conglutin fractions of lupin. The secondary structures of the selected aptamers were predicted using m-fold. Finally, the functionality of the selected aptamers was demonstrated using a competitive assay for the quantitative detection of ß-conglutin. . Future work will focus on structure elucidation and truncation of the selected sequences to generate a smaller aptamer for application to the analysis of the Lup an 1 allergen in foodstuffs.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
High-risk pathogens such as Francisella tularensis and Yersinia pestis are categorized as highly hazardous organisms that can be used as biological weapons. Given the extreme infectivity of these ...potential biowarfare agents, a rapid, sensitive, cost-effective, and specific method for their detection is required. Here, we report the multiplexed amplification detection of genomic DNA from Francisella tularensis and Yersinia pestis. Amplification was achieved using isothermal recombinase polymerase amplification, exploiting tailed primers, followed by detection using a nucleic-acid lateral flow assay. Excess primers were removed using a novel fishing strategy, avoiding the use of postamplification purification that requires centrifugation and infers additional assay cost. The entire assay is completed in less than 1 h, achieving limits of detection of 243 fg (1.21 × 102 genome equivalent) and 4 fg (0.85 genome equivalent) for Francisella tularensis and Yersinia pestis, respectively.
A bifunctional derivative of the thrombin-binding aptamer with a redox-active Fc moiety and a thiol group at the termini of the aptamer strand was synthesized. The ferrocene-labeled aptamer thiol was ...self-assembled through S−Au bonding on a polycrystalline gold electrode surface and the surface was blocked with 2-mercaptoethanol to form a mixed monolayer. By use of a fluorescent molecular beacon, the effect of counterions on quadruplex formation was established. The aptamer-modified electrode was characterized electrochemically by cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrochemical impedance spectroscopy (EIS). The modified electrode showed a voltammetric signal due to a one-step redox reaction of the surface-confined ferrocenyl moiety of the aptamer immobilized on the electrode surface in 10 mM N-(2-hydroxyethyl)piperazine-N‘-2-ethanesulfonic acid (HEPES) buffer of pH 8.0. An increase in the DPV current signal was evident after blocking with 2-mercaptoethanol, effectively removing aptamer nonspecifically absorbed rather than bound to electrode surface or due to the formation of the aptamer−thrombin affinity interaction. The impedance measurement, in agreement with the differential pulse voltammetry (DPV), showed decreased Faradaic resistances in the same sequence. The “signal-on” upon thrombin association could be attributed to a change in conformation from random coil-like configuration on the probe-modified film to the quadruplex structure. The DPV of the modified electrode showed a linear response of the Fc oxidation signal to the increase in the thrombin concentration in the range between 5.0 and 35.0 nM with a linear correlation of r = 0.9988 and a detection limit of 0.5 nM. The molecular beacon aptasensor was amenable to full regeneration by simply unfolding the aptamer in 1.0 M HCl, and could be regenerated 25 times with no loss in electrochemical signal upon subsequent thrombin binding.
The objective of the current study was to examine phenotypic fertility performance and survival, and to gain insight into underlying factors that may contribute to greater fertility performance in 2 ...divergent genetic groups (GG) of Holstein-Friesian, selected using the Irish Economic Breeding Index (EBI). The GG were evaluated across 3 spring calving pasture-based feeding treatments (FT) over 4 yr. The 2 divergent GG were (1) high EBI; representative of the top 5% nationally (elite), and (2) EBI representative of the national average (NA). In each year, 90 elite and 45 NA cows were randomly allocated to 1 of 3 FT: control, lower grass allowance, and high concentrate. No interaction between GG and FT was observed for any of the measures of fertility investigated. The elite cows achieved significantly greater pregnancy rate to first service (+14.9 percentage points), and significantly greater pregnancy rates after 21, 42, and 84 d of breeding (+17.3, +15.2, and +9.6 percentage points, respectively) compared with NA. The number of services per cow was fewer for elite (1.57) compared with NA (1.80). The interval from mating start date to pregnancy was significantly shorter for elite cows compared with NA. The elite cows maintained greater mean body condition score than NA throughout the study (2.91 vs. 2.72), and had greater body condition score at calving, artificial insemination, and drying off compared with NA. The elite cows had greater mean circulating concentrations of insulin-like growth factor-1 compared with NA. No significant effect was observed of GG on commencement of luteal activity, or progesterone profile variables. Greater survival to the start of fifth lactation was observed for elite cows. The elite cows were 43% less likely to be culled than NA by the beginning of the fifth lactation. The results highlight the success of the Economic Breeding Index to deliver reproductive performance and longevity consistent with industry targets across a range of seasonal pasture-based FT. The results also clearly demonstrate the potential of appropriate genetic selection to reverse negative fertility trends incurred during previous decades of selection for milk production alone.
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